SMTL ID : 9bsn.1

Structure of human K2P13.1 (THIK-1) in lipid nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x D12: DODECANE(Non-functional Binders)

D12.1: 8 residues within 4Å: Chain A: F.101, R.258, F.259, F.262 Chain B: V.28 Ligands: OCT.5, OCT.6, EIC.9 No protein-ligand interaction detected (PLIP) D12.13: 5 residues within 4Å: Chain A: V.28 Chain B: F.101, R.258 Ligands: OCT.18, EIC.22 No protein-ligand interaction detected (PLIP)

8 x D10: DECANE(Non-functional Binders)

D10.2: 5 residues within 4Å: Chain A: F.145, R.148, I.152 Chain B: N.17 Ligands: D10.12 No protein-ligand interaction detected (PLIP) D10.3: 4 residues within 4Å: Chain A: S.253, L.256, A.260 Ligands: D10.4 No protein-ligand interaction detected (PLIP) D10.4: 4 residues within 4Å: Chain A: C.211, A.214, M.215 Ligands: D10.3 No protein-ligand interaction detected (PLIP) D10.10: 4 residues within 4Å: Chain A: N.17, L.21 Ligands: D10.14, EIC.22 No protein-ligand interaction detected (PLIP) D10.12: 4 residues within 4Å: Chain B: N.17, L.21 Ligands: D10.2, EIC.9 No protein-ligand interaction detected (PLIP) D10.14: 4 residues within 4Å: Chain A: N.17 Chain B: R.148, I.152 Ligands: D10.10 No protein-ligand interaction detected (PLIP) D10.15: 3 residues within 4Å: Chain B: L.256, A.260 Ligands: D10.16 No protein-ligand interaction detected (PLIP) D10.16: 5 residues within 4Å: Chain B: C.211, A.214, M.215 Ligands: D10.15, OCT.19 No protein-ligand interaction detected (PLIP)

10 x OCT: N-OCTANE(Non-functional Binders)

OCT.5: 3 residues within 4Å: Chain A: G.255, F.259 Ligands: D12.1 No protein-ligand interaction detected (PLIP) OCT.6: 1 residues within 4Å: Ligands: D12.1 No protein-ligand interaction detected (PLIP) OCT.7: 4 residues within 4Å: Chain A: C.210, C.211, A.214, Y.224 No protein-ligand interaction detected (PLIP) OCT.8: 2 residues within 4Å: Chain A: G.122, F.126 No protein-ligand interaction detected (PLIP) OCT.11: 3 residues within 4Å: Chain A: F.97 Chain B: L.32, G.33 No protein-ligand interaction detected (PLIP) OCT.17: 2 residues within 4Å: Chain B: G.255, F.259 No protein-ligand interaction detected (PLIP) OCT.18: 2 residues within 4Å: Chain B: F.97 Ligands: D12.13 No protein-ligand interaction detected (PLIP) OCT.19: 4 residues within 4Å: Chain B: C.211, A.214, Y.224 Ligands: D10.16 No protein-ligand interaction detected (PLIP) OCT.20: 2 residues within 4Å: Chain B: G.122, F.126 No protein-ligand interaction detected (PLIP) OCT.21: 3 residues within 4Å: Chain A: L.32, G.33 Chain B: F.97 No protein-ligand interaction detected (PLIP)

2 x EIC: LINOLEIC ACID(Non-covalent)

EIC.9: 21 residues within 4Å: Chain A: F.101, Y.102, G.105, T.106, V.108, S.109, I.111, T.138, F.141, S.246, R.258, N.261, F.262, I.265, L.266 Chain B: A.24, I.27, V.28, L.31 Ligands: D12.1, D10.12 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.102, A:F.262, A:I.265, A:I.265, A:L.266, B:I.27 Hydrogen bonds: A:S.246, A:N.261 Salt bridges: A:R.92 EIC.22: 20 residues within 4Å: Chain A: A.24, I.27, V.28, L.31 Chain B: F.101, Y.102, G.105, T.106, V.108, S.109, I.111, T.138, F.141, R.258, N.261, F.262, I.265, L.266 Ligands: D10.10, D12.13 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.102, B:Y.102, B:F.262, B:F.262, B:I.265, A:I.27 Hydrogen bonds: B:N.261 Salt bridges: B:R.92

4 x K: POTASSIUM ION(Non-covalent)

K.23: 9 residues within 4Å: Chain A: G.112, F.113, G.239, F.240 Chain B: G.112, F.113, G.239, F.240 Ligands: K.26 No protein-ligand interaction detected (PLIP) K.24: 10 residues within 4Å: Chain A: T.110, I.111, T.237, I.238 Chain B: T.110, I.111, T.237, I.238 Ligands: K.25, K.26 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:I.111, A:I.238, B:I.111, B:I.238 K.25: 5 residues within 4Å: Chain A: T.110, T.237 Chain B: T.110, T.237 Ligands: K.24 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:T.110, A:T.237, B:T.110, B:T.237 K.26: 10 residues within 4Å: Chain A: I.111, G.112, I.238, G.239 Chain B: I.111, G.112, I.238, G.239 Ligands: K.23, K.24 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:G.112, A:G.239, B:G.112, B:G.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roy-Chowdhury, S. et al., Structure of the human K 2P 13.1 channel reveals a hydrophilic pore restriction and lipid cofactor site. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-02-26

Peptides

Potassium channel subfamily K member 13: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
U

B
A

Membrane

We predict this structure to be a membrane protein.
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Potassium channel subfamily K member 13

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